Fast and sensitive taxonomic classification for metagenomics with Kaiju
Identifieur interne : 001254 ( Main/Exploration ); précédent : 001253; suivant : 001255Fast and sensitive taxonomic classification for metagenomics with Kaiju
Auteurs : Peter Menzel [Danemark] ; Kim Lee Ng [Danemark] ; Anders Krogh [Danemark]Source :
- Nature Communications [ 2041-1723 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Proteins.
- classification : Metagenomics.
- Algorithms, Amino Acid Sequence, Animals, Classification, Humans, Metagenome.
Abstract
Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic
Url:
DOI: 10.1038/ncomms11257
PubMed: 27071849
PubMed Central: 4833860
Affiliations:
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strict</wicri:regionArea></affiliation></author><author><name sortKey="Krogh, Anders" sort="Krogh, Anders" uniqKey="Krogh A" first="Anders" last="Krogh">Anders Krogh</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Biology, University of Copenhagen</institution>, Copenhagen 2200,<country>Denmark</country></nlm:aff><country xml:lang="fr">Danemark</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27071849</idno><idno type="pmc">4833860</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833860</idno><idno type="RBID">PMC:4833860</idno><idno type="doi">10.1038/ncomms11257</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000140</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000140</idno><idno type="wicri:Area/Pmc/Curation">000140</idno><idno 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type="wicri:Area/Main/Exploration">001254</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Fast and sensitive taxonomic classification for metagenomics with Kaiju</title><author><name sortKey="Menzel, Peter" sort="Menzel, Peter" uniqKey="Menzel P" first="Peter" last="Menzel">Peter Menzel</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Biology, University of Copenhagen</institution>, Copenhagen 2200,<country>Denmark</country></nlm:aff><country xml:lang="fr">Danemark</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Ng, Kim Lee" sort="Ng, Kim Lee" uniqKey="Ng K" first="Kim Lee" last="Ng">Kim Lee Ng</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Biology, University of Copenhagen</institution>, Copenhagen 2200,<country>Denmark</country></nlm:aff><country xml:lang="fr">Danemark</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Krogh, Anders" sort="Krogh, Anders" uniqKey="Krogh A" first="Anders" last="Krogh">Anders Krogh</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Biology, University of Copenhagen</institution>, Copenhagen 2200,<country>Denmark</country></nlm:aff><country xml:lang="fr">Danemark</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Nature Communications</title><idno type="eISSN">2041-1723</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Amino Acid Sequence</term><term>Animals</term><term>Classification</term><term>Humans</term><term>Metagenome</term><term>Metagenomics (classification)</term><term>Proteins (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Animaux</term><term>Classification</term><term>Humains</term><term>Métagénome</term><term>Métagénomique ()</term><term>Protéines ()</term><term>Séquence d'acides aminés</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Proteins</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Metagenomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Amino Acid Sequence</term><term>Animals</term><term>Classification</term><term>Humans</term><term>Metagenome</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Animaux</term><term>Classification</term><term>Humains</term><term>Métagénome</term><term>Métagénomique</term><term>Protéines</term><term>Séquence d'acides aminés</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic <italic>k</italic>-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows–Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current <italic>k</italic>-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at <ext-link ext-link-type="uri" xlink:href="http://kaiju.binf.ku.dk">http://kaiju.binf.ku.dk</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Riesenfeld, C" uniqKey="Riesenfeld C">C. Riesenfeld</name></author><author><name sortKey="Schloss, P" uniqKey="Schloss P">P. Schloss</name></author><author><name sortKey="Handelsman, J" uniqKey="Handelsman J">J. Handelsman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shokralla, S" uniqKey="Shokralla S">S. Shokralla</name></author><author><name sortKey="Spall, J" uniqKey="Spall J">J. Spall</name></author><author><name sortKey="Gibson, J" uniqKey="Gibson J">J. Gibson</name></author><author><name sortKey="Hajibabaei, M" uniqKey="Hajibabaei M">M. Hajibabaei</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Segata, N" uniqKey="Segata N">N. 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